The growing influence of evangelical Protestants is roiling the military chaplain corps, where their desire to preach their faith more openly is colliding with long-held military traditions of pluralism and diversity.

After accusations this summer that evangelical chaplains, faculty and coaches were pressuring cadets at the Air Force Academy, the Air Force yesterday issued new guidelines on respect for religious minorities. In the Navy, evangelical Protestant chaplains are fighting what they say is a legacy of discrimination in hiring and promotions, and they are bridling at suggestions they not pray publicly "in the name of Jesus."

Much of the conflict is in two areas that, until now, have been nearly invisible to civilians: how the military hires its ministers and how they word their public prayers. Evangelical chaplains -- who are rising in numbers and clout amid a decline in Catholic priests and mainline Protestant ministers -- are challenging the status quo on both questions, causing even some evangelical commanders to worry about the impact on morale.

"There is a polarization that is beginning to set up that I don't think is helpful. Us versus them," said Air Force Col. Richard K. Hum, an Evangelical Free Church minister who is the executive director of the Armed Forces Chaplains Board. "I don't know whether it's an overflow of what's happening in society. But this sort of thing is so detrimental to what we are trying to do in the chaplaincy."

The Rev. MeLinda S. Morton, a Lutheran minister who resigned in June as an Air Force chaplain after criticizing the religious atmosphere at the Air Force Academy, said there has been a palpable rise in evangelical fervor not just among chaplains but also among the officer corps in general since she joined the military in 1982, originally as a launch officer in a nuclear missile silo.

"When we were coneheads -- missile officers -- I would never, ever have engaged in conversations with subordinates aligning my power and position as an officer with my views on faith matters," she said. Today, "I've heard of people being made incredibly uncomfortable by certain wing commanders who engage in sectarian devotions at staff meetings."

Diversity Without Quotas

The tradition of chaplains in the U.S. military goes back to George Washington, who first sought a minister for his Virginia regiment in 1756. In the early days of the republic, commanders simply chose a chaplain who shared their beliefs. But with the expansion of the military in World War II, the armed services set quotas for chaplains of various faiths, attempting to match the proportion of each denomination in the general population.

In a class-action lawsuit -- filed in 1999 in U.S. District Court for the District of Columbia and still in the discovery, or evidence-gathering, stage -- more than 50 Navy chaplains contend that the formula became a rigid and discriminatory "thirds rule": one-third Catholics, one-third mainline Protestants and one-third everybody else.

According to Hum, the military abandoned numerical targets about 20 years ago, partly for legal reasons and partly because the proliferation of religious groups made the system unworkable. Although chaplains are paid by the armed services, they must be ordained and "endorsed," or nominated, by religious organizations. The number of endorsers has grown from about 10 denominations in 1945 to more than 240 groups today, Hum said.

Like college admissions officers, Pentagon officials now say they seek diversity without using quotas.

"We don't actually say we want to have four rabbis this year, or 20 Catholic priests. What we do is, we look at who is sent to us by our endorsers throughout the country and . . . then we bring the best qualified into the chaplain corps," Rear Adm. Louis V. Iasiello, a Catholic priest and the chief of Navy chaplains, said in an interview at the Pentagon's Navy Annex.

Pentagon data analyzed by The Washington Post show a substantial rise in the number of evangelical chaplains in the past decade, along with a modest decline in mainline Protestant ministers and a precipitous drop in Catholic priests, mirroring a nationwide priest shortage.